A Letter Concerning the Present State of Religion Amongst us; [Under the Act of Establishment, prosecuted by the Ordinances constituting the Triers, and Commissioners for ejecting of Scandalous Ministers:] 8vo. pp. 24. n. p. or date and anonymously, but published first in 1656; [avowed by the author, and republished with alterations and the additional clause added to the title-page, at the end of Just Weights and Measures, 1662, and 1680. 4to.]
The Due Way of Composing the Differences on Foot, preserving the Church; according to the Opinion of Herbert Thorndike. London: Printed by A. Warren, for John Martin, James Allestry, and Thomas Dicas, at the Bell in St. Paul's Church-yard, 1660. small 8vo. [and again at the end of Just Weights and Measures, 1662, and 1680. 4to.]
Just Weights and Measures: that is, The Present State of Religion weighed in the balance, and measured by the standard of the Sanctuary; according to the opinion of Herbert Thorndike. London: Printed for J. M. for J. Martin, J. Allestry, and T. Dicas, and are to be sold at the sign of the Bell in St. Paul's Church-yard, 1662. 4to. [And second edition: printed by S. Roycroft for J. Martyn. 1680. 4to.]
The True Principle of Comprehension: or a Petition against the Presbyterian Request for a Comprehensive Act, in 1667: [now first published.]
The Plea of Weakness and Tender Consciences Discussed and Answered: in a Discourse upon Rom. xv. 1: [written in 1667/8: now first published.]
A Discourse of the Forbearance or the Penalties which a Due Reformation Requires: by H. Thorndike, one of the Prebends of Westminster Church. London: Printed by J. M. for James Collins, at the Kings-Head in Westminster Hall, 1670. Small 8vo.
The Reformation of the Church of England better than that of the Council of Trent: or a Short Resolution of the Controversies between the Churches of England and Rome: [written in 1670-2: now first published.]
Mr. Herbert Thorndike's judgment of the Church of Rome: [published ater the writer's death by Stillingfleet in his Conferences between a Romish Priest, a Fanatic Chaplain, and a Divine of the Church of England, concerning the Idolatry in the Church of Rome, pp. 85 sq., 8vo. Lond. 1679.]